MolNFT v1 · #129321 · protein
Structure of cathepsin B1 from schistosoma mansoni in complex with WRR286 inhibitor
5OGR · Cathepsin B-like peptidase (C01 family): “Structure of cathepsin B1 from schistosoma mansoni in complex with WRR286 inhibitor”. X-ray diffraction, 1 ligand (VS4), 7 pockets (best druggability 0.76). MolNFT v1 #129321 on GenesisL1…
- PDB
- 5OGR
- Type
- protein
- Length
- 762 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B-like peptidase (C01 family)
- UniProt
- Q8MNY2
- Ligands
- VS4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cathepsin B-like peptidase (C01 family) | protein | 254 | 27% helix, 23% strand | Q8MNY2 |
Ligands and binding sites
- VS4 · 3-[[N-[4-methyl-piperazinyl]carbonyl]-phenylalaninyl-amino]-5-phenyl-pentane-1-sulfonic acid benzyloxy-amide · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.76 | 0.79 | 82 | ACT, VS4 |
| 2 | 267 | 0.55 | 0.77 | 33 | VS4 |
| 3 | 223 | 0.53 | 0.77 | 27 | VS4 |
| 4 | 51 | 0.45 | 0.85 | 23 | empty |
| 5 | 63 | 0.34 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 373 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 146 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
- 5OGR · Structure of cathepsin B1 from Schistosoma mansoni in complex with WRR286 inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8MNY2
- Elsewhere: RCSB PDB 5OGR · PDBe 5OGR · UniProt Q8MNY2
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